vcf header does not include CN1

Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data

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vcf header does not include CN1 #122

Closed jazberna1 closed 5 years ago

jazberna1 commented 5 years ago

Hello,

I have sucessfully run SmallPedigree-WGS. I have noticed the vcf header does not include CN1 as option for the ALT field.

Is this expected and I am just missinterpreting the output?

Many thanks Jorge

eroller commented 5 years ago

CN1 is the reference allele. So GT=0/0 would mean one copy on each chromosome. It is a little misleading because Canvas does not actually determine with certainty what the copy number is on each chromosome. For interpretation of variant calls it is best to just look at the overall copy number (the CN field in the genotype column)

jazberna1 commented 5 years ago

Hello Eric,

Thanks so much for the explanation! Jorge